Thanks Bernie...I just rechecked this guy, and the latest mapping from 1kG does indeed show L621+ as you suspected. On Wed, Jan 8, 2014 at 7:36 PM, Bernie Cullen <[email protected]>wrote: > Greg, I see this note about HG00360 at the spreadsheet: > "I2a-M423, L147+, L69.2+, P41/M359-; originally listed as L621+, but GregRM > can't find any evidence of this in mapped sequence data" > > Still I think it's very likely that he is L621+ and a normal Dinaric (this > occurrence L147 is supposed to be downstream of L621 after all). > > Bernie > > > On Wed, Jan 8, 2014 at 7:28 PM, G. Magoon <[email protected]> wrote: > > > HG00360: M423+, L147+, L69.2+, P41/M359-, L621+, L178+, along with being > > derived for a number of other CTS/Z SNPs > > PGP64: L161+ > > PGP119: L161+ > > PGP125: L621+ > > > > > > On Wed, Jan 8, 2014 at 7:13 PM, Kenneth Nordtvedt < > [email protected] > > >wrote: > > > > > Here are four “public” dna samples for which full genomes have been > > > measured. > > > > > > Do you know their haplogroup designation? > > > > > > HG00360 > > > PGP64 > > > PGP119 > > > PGP125 > > > > > > I am hoping they include both L161+ Isles clades and L621 dinaric > clade. > > > > > > > > > > > > Kenneth Nordtvedt > > > > > > Haplogroup I Clade Modalities and Trees at: > > > http://knordtvedt.home.bresnan.net > > > > > > > > > ------------------------------- > > > To unsubscribe from the list, please send an email to > > > [email protected] with the word 'unsubscribe' > > > without the quotes in the subject and the body of the message > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > > > > > -- > ---I read every email but I'm not always able to respond immediately. If > you think you've been waiting too long for a reply, please, email me again > at [email protected] > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Greg, I see this note about HG00360 at the spreadsheet: "I2a-M423, L147+, L69.2+, P41/M359-; originally listed as L621+, but GregRM can't find any evidence of this in mapped sequence data" Still I think it's very likely that he is L621+ and a normal Dinaric (this occurrence L147 is supposed to be downstream of L621 after all). Bernie On Wed, Jan 8, 2014 at 7:28 PM, G. Magoon <[email protected]> wrote: > HG00360: M423+, L147+, L69.2+, P41/M359-, L621+, L178+, along with being > derived for a number of other CTS/Z SNPs > PGP64: L161+ > PGP119: L161+ > PGP125: L621+ > > > On Wed, Jan 8, 2014 at 7:13 PM, Kenneth Nordtvedt <[email protected] > >wrote: > > > Here are four “public” dna samples for which full genomes have been > > measured. > > > > Do you know their haplogroup designation? > > > > HG00360 > > PGP64 > > PGP119 > > PGP125 > > > > I am hoping they include both L161+ Isles clades and L621 dinaric clade. > > > > > > > > Kenneth Nordtvedt > > > > Haplogroup I Clade Modalities and Trees at: > > http://knordtvedt.home.bresnan.net > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] with the word 'unsubscribe' > > without the quotes in the subject and the body of the message > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message > -- ---I read every email but I'm not always able to respond immediately. If you think you've been waiting too long for a reply, please, email me again at [email protected]

HG00360: M423+, L147+, L69.2+, P41/M359-, L621+, L178+, along with being derived for a number of other CTS/Z SNPs PGP64: L161+ PGP119: L161+ PGP125: L621+ On Wed, Jan 8, 2014 at 7:13 PM, Kenneth Nordtvedt <[email protected]>wrote: > Here are four “public” dna samples for which full genomes have been > measured. > > Do you know their haplogroup designation? > > HG00360 > PGP64 > PGP119 > PGP125 > > I am hoping they include both L161+ Isles clades and L621 dinaric clade. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message

The list of I phyloequivalents could be very useful. Thank you for suppling it. Could you explain the no asterix, one asterix. two ...... rating system. Everything I have seen is technical goobly gook talk to me. Can it be reexplained in plain English. "Number of reads" by itself means nothing by itself to me. Is the same piece of lab guuu being read over and over? That would be sort of a waste of time; wouldn't you get the same result if reading the same stuff over and over? If number of reads is to mean anything important it must be independent reads on different stuff which under some model or theory should be yielding the same output. "Independence" of the operations is key. So please; how does the asterix rating system really operate, and how do they lead to the percentages, whatever they mean. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: G. Magoon Sent: Wednesday, January 08, 2014 3:08 PM To: y-dna-haplogroup-i Subject: Re: [yDNAhgI] Update on Ancient I in Europe Very interesting Ken. Hopefully the raw data for these ancient samples will eventually become available, possibly once the paper is published. If people are looking for a list of phyloequivalent SNPs to the upstream branches like I, IJ, Q, etc., then the supporting info (Supporting Info B) from the tree generated for our recent manuscript ( http://biorxiv.org/content/early/2013/12/13/000802) should be useful. For example, here are all the SNPs on the I branch with P38: (The more unstable sites have higher "# of mutations in tree".) > For the branch from node 37 to node 4 with length 7090.00: > 2688442 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS48', 'PF3569'] > 2707072 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > ['CTS70', 'PF3570'] > 2723755 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS88', 'PF3571'] > 2884029 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['L844', 'PF3572', 'YSC0000275'] > 2974782 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3574'] > 3003354 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3575'] > 3315632 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 3366638 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3578'] > 3545070 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['P212', 'PF3580'] > 3831248 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3585'] > 3851589 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3586'] > 3928388 REF->ALT (G->T); # of mutations in tree = 3 (weighted = 15) > 3932370 REF->ALT (TAA->TA); # of mutations in tree = 1 (weighted = 35) > 3938321 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 4064632 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['PF3588'] > 4077210 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3589'] > 4116203 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3590'] > 4180074 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 4184066 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3592'] > 4245332 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3594'] > 4748471 REF->ALT (A->G); # of mutations in tree = 2 (weighted = 70) > 4859526 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3599'] > 4974832 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 4989857 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3600'] > 5129448 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 0); > ['PF3601'] > 5129449 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 0) > 5196541 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['PF3602'] > 5197625 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35); > ['PF3603'] > 5206105 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3604'] > 5217196 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3605'] > 5514820 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 70) > 5528525 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 5586317 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35); > ['PF3611'] > 5643555 REF->ALT (T->G); # of mutations in tree = 2 (weighted = 70); > ['PF3612'] > 5729506 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 5744201 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 5772273 REF->ALT (T->C); # of mutations in tree = 3 (weighted = 15) > 5857698 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3616'] > 5925267 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3617'] > 6067284 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3618'] > 6422345 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3620'] > 6440847 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3622'] > 6477593 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3625'] > 6489980 REF->ALT (T->A); # of mutations in tree = 2 (weighted = 70) > 6497838 REF->ALT (GAA->GAAA); # of mutations in tree = 2 (weighted = 70) > 6575427 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 6662712 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3627', 'V218'] > 6926038 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS646', 'PF3629'] > 6943522 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS674', 'PF3630'] > 7004291 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35); > ['CTS772', 'PF3631'] > 7137088 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS1006'] > 7203486 REF->ALT (CTGT->CT); # of mutations in tree = 1 (weighted = 35) > 7321418 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS1301', 'PF3635'] > 7438521 REF->ALT (G->C); # of mutations in tree = 3 (weighted = 0); > ['CTS1491'] > 7438523 REF->ALT (G->C); # of mutations in tree = 3 (weighted = 0); > ['CTS1492'] > 7570370 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3639'] > 7642823 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35) > 7681156 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['PF3640'] > 7688470 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3641'] > 7712917 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3642'] > 7853028 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['PF3645'] > 7856500 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L846', 'PF3646', 'YSC0000280'] > 7898045 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3864'] > 8046731 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3649'] > 8262092 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 8267857 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['L578', 'PF3653'] > 8278628 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3654'] > 8382265 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['YSC0000281'] > 8465165 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L755', 'PF3659', 'YSC0000283'] > 8466652 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3660'] > 8484606 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['PF3661'] > 8485677 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['L756', 'PF3662', 'YSC0000284'] > 8536868 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['L758', 'PF3663', 'YSC0000285'] > 8643763 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3665'] > 8728974 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['PF3666'] > 8873160 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3668'] > 8984184 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3670'] > 9398607 REF->ALT (G->T); # of mutations in tree = 11 (weighted = 0); > ['M7449', 'PF3673'] > 9420891 REF->ALT (A->ACC); # of mutations in tree = 1 (weighted = 35) > 9516653 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['PF3675'] > 9827411 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['YSC0000256'] > 9832636 REF->ALT (A->G); # of mutations in tree = 5 (weighted = 0); > ['PF3676'] > 9891668 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3677'] > 9900057 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 10051801 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 13430863 REF->ALT (G->A); # of mutations in tree = 4 (weighted = 0) > 13442439 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 13492708 REF->ALT (GTT->GTTT); # of mutations in tree = 3 (weighted = 15) > 13544835 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3685'] > 13610767 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3687'] > 13642029 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3689'] > 13804066 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35) > 13835003 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 13900590 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3694'] > 13914715 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3695'] > 13961890 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS1555', 'PF3696'] > 14073053 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['CTS1800', 'PF3699'] > 14214481 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['CTS2193', 'PF3703'] > 14286853 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS2387', 'PF3705'] > 14337364 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS2514', 'PF3706'] > 14352669 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS2536', 'PF3707'] > 14484379 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['P38', 'PF3708'] > 14646409 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS3076', 'PF3712'] > 14847792 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['M170', 'PF3715'] > 14884646 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 0); > ['CTS3383', 'PF3716'] > 14884659 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 0); > ['CTS3384', 'PF3717'] > 14974451 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > ['L1197', 'PF3718', 'YSC0000260'] > 14986989 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['CTS3517', 'PF3719'] > 15023364 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['M258', 'PF3721'] > 15089989 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > ['CTS3641', 'PF3722'] > 15377802 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4077', 'PF3725'] > 15389836 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4088', 'PF3868'] > 15479899 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4209', 'PF3726'] > 15506055 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4239', 'PF3727'] > 15536759 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4272', 'PF3728'] > 15536870 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS4273', 'PF3729'] > 15595624 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4340', 'PF3730'] > 15615533 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['L772', 'PF3731', 'YSC0000263'] > 15742130 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4637'] > 15759200 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4664'] > 15793946 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4745', 'PF3734'] > 15859012 REF->ALT (TCCC->TCC); # of mutations in tree = 1 (weighted = 35) > 15862842 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS4848', 'PF3736'] > 15937959 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS4982', 'PF3737'] > 15960476 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5016', 'PF3738'] > 16039881 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > ['CTS5150', 'PF3739'] > 16131227 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70) > 16171560 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS5263'] > 16354708 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3742', 'U179'] > 16397716 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS5622', 'PF3743'] > 16415916 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5650', 'PF3744'] > 16471254 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5764', 'PF3746'] > 16548548 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['CTS5908', 'PF3747'] > 16567253 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5946', 'PF3748'] > 16575110 REF->ALT (AT->A); # of mutations in tree = 1 (weighted = 35) > 16751000 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS6231', 'PF3750'] > 16780748 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS6265', 'PF3871'] > 16785944 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > ['CTS6271', 'PF3751'] > 16826642 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS6334', 'PF3752'] > 16836079 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS6343', 'PF3753'] > 16836548 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS6344', 'PF3754'] > 16939794 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['CTS6497', 'PF3756'] > 17090238 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS6751', 'PF3757'] > 17245841 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS7026', 'PF3758'] > 17424807 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS7329'] > 17467526 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3759', 'YSC0000267'] > 17497181 REF->ALT (C->A); # of mutations in tree = 2 (weighted = 70); > ['CTS7469'] > 17511797 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS7502', 'PF3760'] > 17525137 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS7540', 'PF3761'] > 17548890 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS7593', 'PF3763'] > 17622756 REF->ALT (A->C); # of mutations in tree = 9 (weighted = 0); > SITEOF(['M9222']) > 17692855 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS7831', 'PF3766'] > 17818847 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8064', 'PF3768'] > 17901509 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8257'] > 17924382 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8300', 'PF3770'] > 17940414 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8333', 'PF3771'] > 17949402 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS8345', 'PF3772'] > 18018313 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8420', 'PF3773'] > 18078759 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8545', 'PF3775'] > 18172947 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS8742', 'PF3776'] > 18257568 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8876', 'PF3778'] > 18394743 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['L751', 'PF3779', 'YSC0000291'] > 18404486 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3780'] > 18582617 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS8963'] > 18786174 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS9264', 'PF3782'] > 18789763 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS9269', 'PF3783'] > 18927031 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS9484', 'PF3785'] > 18992894 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS9618', 'PF3786'] > 19048602 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['L41', 'PF3787'] > 19097563 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS9838', 'PF3788'] > 19104986 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS9860', 'PF3790'] > 19233673 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS10058'] > 19435305 REF->ALT (A->AT); # of mutations in tree = 1 (weighted = 35) > 21067903 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3794'] > 21077471 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3795'] > 21119888 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3796'] > 21130059 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3797'] > 21155653 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 21199929 REF->ALT (A->G); # of mutations in tree = 2 (weighted = 70); > ['PF3799'] > 21359407 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['L503'] > 21402723 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3800'] > 21452125 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3803'] > 21465033 REF->ALT (C->A); # of mutations in tree = 3 (weighted = 15); > ['PF3804'] > 21515724 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 21525069 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3806'] > 21535086 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3807'] > 21556106 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3809'] > 21627180 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3811'] > 21689728 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 21794672 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3813'] > 21839183 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3814'] > 21841289 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3815'] > 21939618 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3817'] > 22100087 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > ['PF3819'] > 22115103 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['YSC0000272'] > 22200336 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3822'] > 22243817 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 22444389 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['PF3827'] > 22458430 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3828'] > 22458740 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3829'] > 22459264 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 22479907 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 22485425 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3833'] > 22525421 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['PF3836'] > 22573702 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3837'] > 22845794 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS10941', 'PF3838'] > 23084562 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['CTS11369', 'PF3840'] > 23113271 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS11441'] > 23154034 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L847', 'PF3841', 'YSC0000298'] > 23156725 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS11540', 'PF3842'] > 23267211 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS11779', 'PF3844'] > 23401471 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS11979', 'PF3878'] > 23479970 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3847', 'YSC0000300'] > 26334890 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 70) > 13246591 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35) On Wed, Jan 8, 2014 at 4:12 PM, Kenneth Nordtvedt <[email protected]>wrote: > Here’s an update on what has recently been learned about haplogroup I ydna > in ancient Europe. Bones of several males from 8000 b.p. were examined > for > their dna: Loschbour was from a Luxuemberg site, four male dna Motala > 2,3,9,12 > were from a Swedish site. Another male from Swedish site, Motala6, seems > not to be confirmed haplogroup I, but his true haplogroup is still > unidentified though thought Q for awhile. Their ydna analysis of these > ancient males is discussed in depth in the paper “Ancient human genomes > suggest three ancestral populations for presentday Europeans”. > > As of a month ago, the hobby community had collected a number of > phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, > L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, > CTS1293, CTS11030. > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades > or from the L621 “Dinaric” clade were found derived for ALL of these 12 > ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > In the cited paper, however, only L178 and M423 were tested on these > ancient dna samples. They took their snps to test from ISOGG list, and as > we know that list always lags present knowledge because of the procedure > of > inclusion into their list. The ancient dna samples are not necessarily > readable on any given snp site, so it is important to have that ancient > dna > tested on alternative sites of equivalence if unreadable on any particular > site. So I sent the 10 snp sites listed above for which they did not test > to authors of the cited paper. They very kindly looked up the allele > values for the additional snps which could be read. > > Loschbour was readable for all 12 snps with results: derived for CTS8239, > CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other > five snps including L1224. > > Motala12 was readable for 9 of the 12 snps with results which exactly > matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > Motala3 was readable for only 3 of the 12 snps with results matching > Loschbour: CTS7218+, CTS176+, CTS1293+ > > Motala2 was readable for only 1 of the 12 snps and disagreed with first > three dna samples, being CTS1293- > > Motala9 was not readable for any of the 12 snps. > > Loschbour and Motala12 (and probably Motala3) establish a new branch line > of the I Tree which is today probably extinct or severely tiny in present > population. It splits the 12 snps into ancestrals and deriveds. See > “Tree and Map for haplogroup I” for position of this new branch of the > tree. > > So we concentrate on what we might further learn about Motala2 and Motala9 > samples using the rich catalog of well placed ysnps that has resulted from > Geno2 and other products done by hobbyists. > > All we know about Motala9 is that he is P38+ but P40-. All we know about > Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are > haplogroup I, but that’s about all we know. > Motala9 could be most anything within haplogroup I except a modern I1. He > could be anything in I2...... and could be a new ancient branch on the > ancestral I1 line which branched off prior to P40. That’s a time range of > 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could > have > branched off of the ancestral I1 line anytime before M253, and Motala > still > has much of I2...... for his location. > > So there is much work that authors of this paper can do using our Geno2 > generated rich lists of phylogenetically equivalent snps for many of the > key branch segments of the I tree. Motala2 and Motala9 could conceivably > be placed fairly well in the haplogroup I tree, giving us much better > incite into presence of our haplogroup in northern Europe 8000 years ago. > I have sent several sets of the confirmed phylogenetically equivalent snp > lists to them and hopefully they will see if they are readable for Motala2 > and Motala9. > > What I have not put together yet, waiting to see if they will use it or > that Motala2 and Motala9 are not confirmed to be part of I2....., is the > very huge list of firmly confirmed phyloequivalent snps to M253 and P40 > (I1 > snps). Since that branch line segment is so long, 22000 years ago up to > 4500 years ago, the list of well confirmed equivalent snps is probably > presently approaching 100 in number. If Motala2 or Motala9 are confirmed > I2..... then no sense checking them on all those I1 snps. > > So there could be much more of value to be extracted from these ancient > dna samples from a complete use of their full genome measurements plus the > hobby community’s most up to date list of well confirmed and well placed > ysnps. > I hope they will continue to work with us as they did on the initial set > of ysnps equivalent to M423 and L178 which produced such informative > results. > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited > paper concluded, then a complete list of phylogenetically equivalent snps > to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Excellent! Many thanks. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: G. Magoon Sent: Wednesday, January 08, 2014 5:28 PM To: y-dna-haplogroup-i Subject: Re: [yDNAhgI] Can you identify these? HG00360: M423+, L147+, L69.2+, P41/M359-, L621+, L178+, along with being derived for a number of other CTS/Z SNPs PGP64: L161+ PGP119: L161+ PGP125: L621+ On Wed, Jan 8, 2014 at 7:13 PM, Kenneth Nordtvedt <[email protected]>wrote: > Here are four “public” dna samples for which full genomes have been > measured. > > Do you know their haplogroup designation? > > HG00360 > PGP64 > PGP119 > PGP125 > > I am hoping they include both L161+ Isles clades and L621 dinaric clade. > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

I know it has turned up as a question on this list on several previous occasions, so I wanted to pass along information that some new Y-STR haplotype data (determined using the conventional electrophoresis approach) for 1000 Genomes Project samples have recently become available from the 1000 Genomes Project: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140107_chrY_str_haplotypes/YSTRs_PowerPLexY23_1000Y_QA_20130107.txt

For what it is worth, an A->C mutation at the site of PF3514 is placed on the IJ branch of the automatically generated phylogeny described in http://biorxiv.org/content/early/2013/12/13/000802, consistent with Obed's observations: > > For the branch from node 3 to node 37 with length 2507.00: > 3074753 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 3110127 REF->ALT (C->G); # of mutations in tree = 4 (weighted = 4) > 3256504 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3503']) > 3496739 REF->ALT (G->A); # of mutations in tree = 3 (weighted = 15) > 3573860 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3504']) > 3850621 REF->ALT (C->A); # of mutations in tree = 3 (weighted = 15); > SITEOF(['PF3505']) > 4050542 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3506']) > 4366933 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3507']) > 4486612 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3508']) > 4520730 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3509'] > 4843178 REF->ALT (A->C); # of mutations in tree = 6 (weighted = 0) > 4860686 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3510'] > 5006360 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3511']) > 5173195 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3512']) > 5558718 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 5578919 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3514']) > 5585882 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70) > 5625159 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 5756437 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3515']) > 5818984 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3517']) > 6607318 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3518']) > 7190277 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 7316588 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS1292'] > 7694266 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 7922133 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3522']) > 7923823 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3523']) > 8222299 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 8558969 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['P130', 'PF3525', 'S22'] > 8590752 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['P127', 'PF3526'] > 8888300 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 8906357 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3528', 'F1460']) > 9921164 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 10002861 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3529']) > 13370245 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3530']) > 13617770 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3531']) > 13637759 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3532']) > 13676377 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3533']) > 13901813 REF->ALT (AC->A); # of mutations in tree = 1 (weighted = 35) > 13906393 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3534']) > 14031334 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['M429', 'P125', 'PF3535'] > 14144593 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['P129', 'PF3536'] > 14214957 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS2197', 'PF3537', 'YSC0001258'] > 15055079 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 15554989 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['F4188', 'PF3539'] > 15887617 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35) > 16244914 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['CTS5387', 'PF3541']) > 16422613 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L775', 'PF3542', 'YSC0000265'] > 16540552 REF->ALT (G->C); # of mutations in tree = 2 (weighted = 70); > ['CTS5899'] > 16674560 REF->ALT (A->G); # of mutations in tree = 2 (weighted = 70); > SITEOF(['CTS6101', 'PF3543']) > 16839810 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70) > 16966024 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 17012180 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['L748', 'PF3546', 'YSC0000289'] > 17040447 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35) > 17200869 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 17513178 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['CTS7507', 'PF3549']) > 18519121 REF->ALT (C->G); # of mutations in tree = 3 (weighted = 15) > 18633084 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['F2794'] > 18769674 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS9240'] > 19038302 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['P124', 'PF3553'] > 19166861 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['F4281', 'P123', 'PF3554'] > 19324937 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS10200'] > 19331026 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS10223'] > 21040853 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3556', 'F3102']) > 21220741 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3557']) > 21225770 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3558']) > 21321273 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3559', 'YSC0001320']) > 21337651 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3560'] > 21389837 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3561']) > 21461202 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3562'] > 21669123 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3563']) > 22319648 REF->ALT (T->G); # of mutations in tree = 2 (weighted = 70) > 22325279 REF->ALT (T->A); # of mutations in tree = 2 (weighted = 70) > 22484240 REF->ALT (G->T); # of mutations in tree = 3 (weighted = 15) > 22883286 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 22909101 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['F3368', 'PF3566', 'YSC0001317'] > 23069523 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 24080237 REF->ALT (A->C); # of mutations in tree = 4 (weighted = 4) > 24426007 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['F3629', 'PF3568'] On Wed, Jan 8, 2014 at 5:00 PM, DNAresults <[email protected]> wrote: > John, > > I might be missing something here, but I agree with Obed -- I am I2b1c > (I-P78) and I have PF 3514 derived (+) from GENO 2.0 as do all the I1d > (I-L22) members of my surname project who tested with GENO 2.0. I don't > have immediate access to the call right now to see if it shows a "C" but I > believe it does. So, no new SNP eh? > > Richard Brewer > > On Wednesday, January 8, 2014, Obed W Odom wrote: > > > John, I wouldn't call PF3514=C a new SNP. I am I1-Z138 and also have C. > In > > fact, the ISOGG Y browser says this SNP is at the IJ level in the Y tree > so > > probably all I and J people should have it. The problem seems to be that > > the original reference for PF3514 showed A to G instead of A to C. All of > > the next-generation-sequencing results that I have seen for I1 and !2 > > people show C. > > > > > > On Wed, Jan 8, 2014 at 2:21 PM, John O'Grady <[email protected] > <javascript:;> > > >wrote: > > > > > Bernie, > > > The reason that the Geno 2.0 chip didn't work is that the PF3514 > mutation > > > is A to C, not A to G. The good news is that, according to Full > Genomes, > > I > > > am PF3514=C+. So we have a new SNP for L161-Isles. > > > John O'Grady > > > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] <javascript:;> with the word > > 'unsubscribe' without the quotes in the subject and the body of the > message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

Here are four “public” dna samples for which full genomes have been measured. Do you know their haplogroup designation? HG00360 PGP64 PGP119 PGP125 I am hoping they include both L161+ Isles clades and L621 dinaric clade. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net

Very interesting Ken. Hopefully the raw data for these ancient samples will eventually become available, possibly once the paper is published. If people are looking for a list of phyloequivalent SNPs to the upstream branches like I, IJ, Q, etc., then the supporting info (Supporting Info B) from the tree generated for our recent manuscript ( http://biorxiv.org/content/early/2013/12/13/000802) should be useful. For example, here are all the SNPs on the I branch with P38: (The more unstable sites have higher "# of mutations in tree".) > For the branch from node 37 to node 4 with length 7090.00: > 2688442 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS48', 'PF3569'] > 2707072 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > ['CTS70', 'PF3570'] > 2723755 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS88', 'PF3571'] > 2884029 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['L844', 'PF3572', 'YSC0000275'] > 2974782 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3574'] > 3003354 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3575'] > 3315632 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 3366638 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3578'] > 3545070 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['P212', 'PF3580'] > 3831248 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3585'] > 3851589 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3586'] > 3928388 REF->ALT (G->T); # of mutations in tree = 3 (weighted = 15) > 3932370 REF->ALT (TAA->TA); # of mutations in tree = 1 (weighted = 35) > 3938321 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 4064632 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['PF3588'] > 4077210 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3589'] > 4116203 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3590'] > 4180074 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 4184066 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3592'] > 4245332 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3594'] > 4748471 REF->ALT (A->G); # of mutations in tree = 2 (weighted = 70) > 4859526 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3599'] > 4974832 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 4989857 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3600'] > 5129448 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 0); > ['PF3601'] > 5129449 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 0) > 5196541 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['PF3602'] > 5197625 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35); > ['PF3603'] > 5206105 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3604'] > 5217196 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3605'] > 5514820 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 70) > 5528525 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 5586317 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35); > ['PF3611'] > 5643555 REF->ALT (T->G); # of mutations in tree = 2 (weighted = 70); > ['PF3612'] > 5729506 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 5744201 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 5772273 REF->ALT (T->C); # of mutations in tree = 3 (weighted = 15) > 5857698 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3616'] > 5925267 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3617'] > 6067284 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3618'] > 6422345 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3620'] > 6440847 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3622'] > 6477593 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3625'] > 6489980 REF->ALT (T->A); # of mutations in tree = 2 (weighted = 70) > 6497838 REF->ALT (GAA->GAAA); # of mutations in tree = 2 (weighted = 70) > 6575427 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 6662712 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3627', 'V218'] > 6926038 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS646', 'PF3629'] > 6943522 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS674', 'PF3630'] > 7004291 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35); > ['CTS772', 'PF3631'] > 7137088 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS1006'] > 7203486 REF->ALT (CTGT->CT); # of mutations in tree = 1 (weighted = 35) > 7321418 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS1301', 'PF3635'] > 7438521 REF->ALT (G->C); # of mutations in tree = 3 (weighted = 0); > ['CTS1491'] > 7438523 REF->ALT (G->C); # of mutations in tree = 3 (weighted = 0); > ['CTS1492'] > 7570370 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3639'] > 7642823 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35) > 7681156 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['PF3640'] > 7688470 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3641'] > 7712917 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3642'] > 7853028 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['PF3645'] > 7856500 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L846', 'PF3646', 'YSC0000280'] > 7898045 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3864'] > 8046731 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3649'] > 8262092 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 8267857 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['L578', 'PF3653'] > 8278628 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3654'] > 8382265 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['YSC0000281'] > 8465165 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L755', 'PF3659', 'YSC0000283'] > 8466652 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3660'] > 8484606 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['PF3661'] > 8485677 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['L756', 'PF3662', 'YSC0000284'] > 8536868 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['L758', 'PF3663', 'YSC0000285'] > 8643763 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3665'] > 8728974 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['PF3666'] > 8873160 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3668'] > 8984184 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3670'] > 9398607 REF->ALT (G->T); # of mutations in tree = 11 (weighted = 0); > ['M7449', 'PF3673'] > 9420891 REF->ALT (A->ACC); # of mutations in tree = 1 (weighted = 35) > 9516653 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['PF3675'] > 9827411 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['YSC0000256'] > 9832636 REF->ALT (A->G); # of mutations in tree = 5 (weighted = 0); > ['PF3676'] > 9891668 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3677'] > 9900057 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 10051801 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 13430863 REF->ALT (G->A); # of mutations in tree = 4 (weighted = 0) > 13442439 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 13492708 REF->ALT (GTT->GTTT); # of mutations in tree = 3 (weighted = 15) > 13544835 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3685'] > 13610767 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3687'] > 13642029 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3689'] > 13804066 REF->ALT (G->C); # of mutations in tree = 1 (weighted = 35) > 13835003 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 13900590 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3694'] > 13914715 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3695'] > 13961890 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS1555', 'PF3696'] > 14073053 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['CTS1800', 'PF3699'] > 14214481 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['CTS2193', 'PF3703'] > 14286853 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS2387', 'PF3705'] > 14337364 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS2514', 'PF3706'] > 14352669 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS2536', 'PF3707'] > 14484379 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['P38', 'PF3708'] > 14646409 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS3076', 'PF3712'] > 14847792 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['M170', 'PF3715'] > 14884646 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 0); > ['CTS3383', 'PF3716'] > 14884659 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 0); > ['CTS3384', 'PF3717'] > 14974451 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > ['L1197', 'PF3718', 'YSC0000260'] > 14986989 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['CTS3517', 'PF3719'] > 15023364 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['M258', 'PF3721'] > 15089989 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > ['CTS3641', 'PF3722'] > 15377802 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4077', 'PF3725'] > 15389836 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4088', 'PF3868'] > 15479899 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4209', 'PF3726'] > 15506055 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4239', 'PF3727'] > 15536759 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4272', 'PF3728'] > 15536870 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS4273', 'PF3729'] > 15595624 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4340', 'PF3730'] > 15615533 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['L772', 'PF3731', 'YSC0000263'] > 15742130 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4637'] > 15759200 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS4664'] > 15793946 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS4745', 'PF3734'] > 15859012 REF->ALT (TCCC->TCC); # of mutations in tree = 1 (weighted = 35) > 15862842 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS4848', 'PF3736'] > 15937959 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS4982', 'PF3737'] > 15960476 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5016', 'PF3738'] > 16039881 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > ['CTS5150', 'PF3739'] > 16131227 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70) > 16171560 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS5263'] > 16354708 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3742', 'U179'] > 16397716 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS5622', 'PF3743'] > 16415916 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5650', 'PF3744'] > 16471254 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5764', 'PF3746'] > 16548548 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['CTS5908', 'PF3747'] > 16567253 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS5946', 'PF3748'] > 16575110 REF->ALT (AT->A); # of mutations in tree = 1 (weighted = 35) > 16751000 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS6231', 'PF3750'] > 16780748 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS6265', 'PF3871'] > 16785944 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > ['CTS6271', 'PF3751'] > 16826642 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS6334', 'PF3752'] > 16836079 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS6343', 'PF3753'] > 16836548 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS6344', 'PF3754'] > 16939794 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['CTS6497', 'PF3756'] > 17090238 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS6751', 'PF3757'] > 17245841 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS7026', 'PF3758'] > 17424807 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS7329'] > 17467526 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3759', 'YSC0000267'] > 17497181 REF->ALT (C->A); # of mutations in tree = 2 (weighted = 70); > ['CTS7469'] > 17511797 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS7502', 'PF3760'] > 17525137 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS7540', 'PF3761'] > 17548890 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS7593', 'PF3763'] > 17622756 REF->ALT (A->C); # of mutations in tree = 9 (weighted = 0); > SITEOF(['M9222']) > 17692855 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS7831', 'PF3766'] > 17818847 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8064', 'PF3768'] > 17901509 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8257'] > 17924382 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8300', 'PF3770'] > 17940414 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8333', 'PF3771'] > 17949402 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS8345', 'PF3772'] > 18018313 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8420', 'PF3773'] > 18078759 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8545', 'PF3775'] > 18172947 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS8742', 'PF3776'] > 18257568 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS8876', 'PF3778'] > 18394743 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['L751', 'PF3779', 'YSC0000291'] > 18404486 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3780'] > 18582617 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS8963'] > 18786174 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS9264', 'PF3782'] > 18789763 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS9269', 'PF3783'] > 18927031 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS9484', 'PF3785'] > 18992894 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS9618', 'PF3786'] > 19048602 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['L41', 'PF3787'] > 19097563 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['CTS9838', 'PF3788'] > 19104986 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS9860', 'PF3790'] > 19233673 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS10058'] > 19435305 REF->ALT (A->AT); # of mutations in tree = 1 (weighted = 35) > 21067903 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3794'] > 21077471 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3795'] > 21119888 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3796'] > 21130059 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3797'] > 21155653 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35) > 21199929 REF->ALT (A->G); # of mutations in tree = 2 (weighted = 70); > ['PF3799'] > 21359407 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['L503'] > 21402723 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3800'] > 21452125 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3803'] > 21465033 REF->ALT (C->A); # of mutations in tree = 3 (weighted = 15); > ['PF3804'] > 21515724 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 21525069 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3806'] > 21535086 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3807'] > 21556106 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3809'] > 21627180 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3811'] > 21689728 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 21794672 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3813'] > 21839183 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3814'] > 21841289 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['PF3815'] > 21939618 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3817'] > 22100087 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > ['PF3819'] > 22115103 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['YSC0000272'] > 22200336 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3822'] > 22243817 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 22444389 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['PF3827'] > 22458430 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['PF3828'] > 22458740 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['PF3829'] > 22459264 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 22479907 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 22485425 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['PF3833'] > 22525421 REF->ALT (T->G); # of mutations in tree = 1 (weighted = 35); > ['PF3836'] > 22573702 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70); > ['PF3837'] > 22845794 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['CTS10941', 'PF3838'] > 23084562 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > ['CTS11369', 'PF3840'] > 23113271 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS11441'] > 23154034 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L847', 'PF3841', 'YSC0000298'] > 23156725 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS11540', 'PF3842'] > 23267211 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS11779', 'PF3844'] > 23401471 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS11979', 'PF3878'] > 23479970 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['PF3847', 'YSC0000300'] > 26334890 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 70) > 13246591 ALT->REF (G->A); # of mutations in tree = 1 (weighted = 35) On Wed, Jan 8, 2014 at 4:12 PM, Kenneth Nordtvedt <[email protected]>wrote: > Here’s an update on what has recently been learned about haplogroup I ydna > in ancient Europe. Bones of several males from 8000 b.p. were examined for > their dna: Loschbour was from a Luxuemberg site, four male dna Motala > 2,3,9,12 > were from a Swedish site. Another male from Swedish site, Motala6, seems > not to be confirmed haplogroup I, but his true haplogroup is still > unidentified though thought Q for awhile. Their ydna analysis of these > ancient males is discussed in depth in the paper “Ancient human genomes > suggest three ancestral populations for presentday Europeans”. > > As of a month ago, the hobby community had collected a number of > phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, > L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, > CTS1293, CTS11030. > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades > or from the L621 “Dinaric” clade were found derived for ALL of these 12 > ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > In the cited paper, however, only L178 and M423 were tested on these > ancient dna samples. They took their snps to test from ISOGG list, and as > we know that list always lags present knowledge because of the procedure of > inclusion into their list. The ancient dna samples are not necessarily > readable on any given snp site, so it is important to have that ancient dna > tested on alternative sites of equivalence if unreadable on any particular > site. So I sent the 10 snp sites listed above for which they did not test > to authors of the cited paper. They very kindly looked up the allele > values for the additional snps which could be read. > > Loschbour was readable for all 12 snps with results: derived for CTS8239, > CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other > five snps including L1224. > > Motala12 was readable for 9 of the 12 snps with results which exactly > matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > Motala3 was readable for only 3 of the 12 snps with results matching > Loschbour: CTS7218+, CTS176+, CTS1293+ > > Motala2 was readable for only 1 of the 12 snps and disagreed with first > three dna samples, being CTS1293- > > Motala9 was not readable for any of the 12 snps. > > Loschbour and Motala12 (and probably Motala3) establish a new branch line > of the I Tree which is today probably extinct or severely tiny in present > population. It splits the 12 snps into ancestrals and deriveds. See > “Tree and Map for haplogroup I” for position of this new branch of the > tree. > > So we concentrate on what we might further learn about Motala2 and Motala9 > samples using the rich catalog of well placed ysnps that has resulted from > Geno2 and other products done by hobbyists. > > All we know about Motala9 is that he is P38+ but P40-. All we know about > Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are > haplogroup I, but that’s about all we know. > Motala9 could be most anything within haplogroup I except a modern I1. He > could be anything in I2...... and could be a new ancient branch on the > ancestral I1 line which branched off prior to P40. That’s a time range of > 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could have > branched off of the ancestral I1 line anytime before M253, and Motala still > has much of I2...... for his location. > > So there is much work that authors of this paper can do using our Geno2 > generated rich lists of phylogenetically equivalent snps for many of the > key branch segments of the I tree. Motala2 and Motala9 could conceivably > be placed fairly well in the haplogroup I tree, giving us much better > incite into presence of our haplogroup in northern Europe 8000 years ago. > I have sent several sets of the confirmed phylogenetically equivalent snp > lists to them and hopefully they will see if they are readable for Motala2 > and Motala9. > > What I have not put together yet, waiting to see if they will use it or > that Motala2 and Motala9 are not confirmed to be part of I2....., is the > very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 > snps). Since that branch line segment is so long, 22000 years ago up to > 4500 years ago, the list of well confirmed equivalent snps is probably > presently approaching 100 in number. If Motala2 or Motala9 are confirmed > I2..... then no sense checking them on all those I1 snps. > > So there could be much more of value to be extracted from these ancient > dna samples from a complete use of their full genome measurements plus the > hobby community’s most up to date list of well confirmed and well placed > ysnps. > I hope they will continue to work with us as they did on the initial set > of ysnps equivalent to M423 and L178 which produced such informative > results. > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited > paper concluded, then a complete list of phylogenetically equivalent snps > to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message

YFull says that HG00360 is L621: http://www.yfull.com/tree/I2a1b3/ John O'Grady > > Greg, I see this note about HG00360 at the spreadsheet: > "I2a-M423, L147+, L69.2+, P41/M359-; originally listed as L621+, but GregRM > can't find any evidence of this in mapped sequence data" > > Still I think it's very likely that he is L621+ and a normal Dinaric (this > occurrence L147 is supposed to be downstream of L621 after all). > > Bernie

Yes, it is derived for the standard snp now for Dinaric I ------ CTS5966 Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Rossa Mullen Sent: Wednesday, January 08, 2014 3:16 PM To: [email protected] Subject: Re: [yDNAhgI] Update on Ancient I in Europe Did you find out any more info on the current Russian sample that was supposed to be similar to one of the old samples? On Wednesday, January 8, 2014 1:20 PM, Kenneth Nordtvedt <[email protected]> wrote: Here’s an update on what has recently been learned about haplogroup I ydna in ancient Europe. Bones of several males from 8000 b.p. were examined for their dna: Loschbour was from a Luxuemberg site, four male dna Motala 2,3,9,12 were from a Swedish site. Another male from Swedish site, Motala6, seems not to be confirmed haplogroup I, but his true haplogroup is still unidentified though thought Q for awhile. Their ydna analysis of these ancient males is discussed in depth in the paper “Ancient human genomes suggest three ancestral populations for presentday Europeans”. As of a month ago, the hobby community had collected a number of phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, CTS1293, CTS11030. Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades or from the L621 “Dinaric” clade were found derived for ALL of these 12 ysnps. Everyone else in haplogroup I was found ancestral for All of them. In the cited paper, however, only L178 and M423 were tested on these ancient dna samples. They took their snps to test from ISOGG list, and as we know that list always lags present knowledge because of the procedure of inclusion into their list. The ancient dna samples are not necessarily readable on any given snp site, so it is important to have that ancient dna tested on alternative sites of equivalence if unreadable on any particular site. So I sent the 10 snp sites listed above for which they did not test to authors of the cited paper. They very kindly looked up the allele values for the additional snps which could be read. Loschbour was readable for all 12 snps with results: derived for CTS8239, CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other five snps including L1224. Motala12 was readable for 9 of the 12 snps with results which exactly matched Loschbour. Unreadable snps were CTS8239, L1224, M423. Motala3 was readable for only 3 of the 12 snps with results matching Loschbour: CTS7218+, CTS176+, CTS1293+ Motala2 was readable for only 1 of the 12 snps and disagreed with first three dna samples, being CTS1293- Motala9 was not readable for any of the 12 snps. Loschbour and Motala12 (and probably Motala3) establish a new branch line of the I Tree which is today probably extinct or severely tiny in present population. It splits the 12 snps into ancestrals and deriveds. See “Tree and Map for haplogroup I” for position of this new branch of the tree. So we concentrate on what we might further learn about Motala2 and Motala9 samples using the rich catalog of well placed ysnps that has resulted from Geno2 and other products done by hobbyists. All we know about Motala9 is that he is P38+ but P40-. All we know about Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are haplogroup I, but that’s about all we know. Motala9 could be most anything within haplogroup I except a modern I1. He could be anything in I2...... and could be a new ancient branch on the ancestral I1 line which branched off prior to P40. That’s a time range of 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could have branched off of the ancestral I1 line anytime before M253, and Motala still has much of I2...... for his location. So there is much work that authors of this paper can do using our Geno2 generated rich lists of phylogenetically equivalent snps for many of the key branch segments of the I tree. Motala2 and Motala9 could conceivably be placed fairly well in the haplogroup I tree, giving us much better incite into presence of our haplogroup in northern Europe 8000 years ago. I have sent several sets of the confirmed phylogenetically equivalent snp lists to them and hopefully they will see if they are readable for Motala2 and Motala9. What I have not put together yet, waiting to see if they will use it or that Motala2 and Motala9 are not confirmed to be part of I2....., is the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 snps). Since that branch line segment is so long, 22000 years ago up to 4500 years ago, the list of well confirmed equivalent snps is probably presently approaching 100 in number. If Motala2 or Motala9 are confirmed I2..... then no sense checking them on all those I1 snps. So there could be much more of value to be extracted from these ancient dna samples from a complete use of their full genome measurements plus the hobby community’s most up to date list of well confirmed and well placed ysnps. I hope they will continue to work with us as they did on the initial set of ysnps equivalent to M423 and L178 which produced such informative results. Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited paper concluded, then a complete list of phylogenetically equivalent snps to P38 should probably be tested to see if he is haplogroup I or not? Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net/ ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Probably the most common usage of "phyloequivalent" would have to mean that for all TESTED modern samples, a set of snps showed derived and ancestral states in unison. We don't know what the entire population turn out to be unless we measured it. So some ancient dna samples might split a phyloequivalence seen in all present day tests, and that is indeed what we saw in the M423 L178 plus 10 more snps case I described. As far as P40 and M253 are concerned, they are on a branch line about 17,500 years long and have dozens and dozens of KNOWN phyloequivalent snps. So P40 and M253 define just two points within that 17500 years branch segment. There could be bones with dna from between those points, prior to both those points, or after both of those points. And concerning those two points, we have not the foggiest idea whether P40 is earlier than M253, or vice versa. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Matthew Simonds Sent: Wednesday, January 08, 2014 3:12 PM To: [email protected] Subject: Re: [yDNAhgI] phyloequivalent ysnps‏ >the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 >(I1 snps)When we talk about SNPs being phyloequivalent, does that only mean >that they are phyloequivalent for modern I1? For example, if all modern I1s >are M253+ P40+ and both SNPs can define haplogroup I1, are we likely to >find some remains eventually that are perhaps P40+ but M253- and represent >some intermediate stage? Matthew Simonds > From: [email protected] > To: [email protected] > Date: Wed, 8 Jan 2014 14:12:40 -0700 > Subject: [yDNAhgI] Update on Ancient I in Europe > > Here’s an update on what has recently been learned about haplogroup I ydna > in ancient Europe. Bones of several males from 8000 b.p. were examined > for their dna: Loschbour was from a Luxuemberg site, four male dna Motala > 2,3,9,12 > were from a Swedish site. Another male from Swedish site, Motala6, seems > not to be confirmed haplogroup I, but his true haplogroup is still > unidentified though thought Q for awhile. Their ydna analysis of these > ancient males is discussed in depth in the paper “Ancient human genomes > suggest three ancestral populations for presentday Europeans”. > > As of a month ago, the hobby community had collected a number of > phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, > L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, > CTS1293, CTS11030. > Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades > or from the L621 “Dinaric” clade were found derived for ALL of these 12 > ysnps. Everyone else in haplogroup I was found ancestral for All of them. > > In the cited paper, however, only L178 and M423 were tested on these > ancient dna samples. They took their snps to test from ISOGG list, and as > we know that list always lags present knowledge because of the procedure > of inclusion into their list. The ancient dna samples are not necessarily > readable on any given snp site, so it is important to have that ancient > dna tested on alternative sites of equivalence if unreadable on any > particular site. So I sent the 10 snp sites listed above for which they > did not test to authors of the cited paper. They very kindly looked up > the allele values for the additional snps which could be read. > > Loschbour was readable for all 12 snps with results: derived for CTS8239, > CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other > five snps including L1224. > > Motala12 was readable for 9 of the 12 snps with results which exactly > matched Loschbour. Unreadable snps were CTS8239, L1224, M423. > > Motala3 was readable for only 3 of the 12 snps with results matching > Loschbour: CTS7218+, CTS176+, CTS1293+ > > Motala2 was readable for only 1 of the 12 snps and disagreed with first > three dna samples, being CTS1293- > > Motala9 was not readable for any of the 12 snps. > > Loschbour and Motala12 (and probably Motala3) establish a new branch line > of the I Tree which is today probably extinct or severely tiny in present > population. It splits the 12 snps into ancestrals and deriveds. See > “Tree and Map for haplogroup I” for position of this new branch of the > tree. > > So we concentrate on what we might further learn about Motala2 and Motala9 > samples using the rich catalog of well placed ysnps that has resulted from > Geno2 and other products done by hobbyists. > > All we know about Motala9 is that he is P38+ but P40-. All we know about > Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are > haplogroup I, but that’s about all we know. > Motala9 could be most anything within haplogroup I except a modern I1. He > could be anything in I2...... and could be a new ancient branch on the > ancestral I1 line which branched off prior to P40. That’s a time range of > 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could > have branched off of the ancestral I1 line anytime before M253, and Motala > still has much of I2...... for his location. > > So there is much work that authors of this paper can do using our Geno2 > generated rich lists of phylogenetically equivalent snps for many of the > key branch segments of the I tree. Motala2 and Motala9 could conceivably > be placed fairly well in the haplogroup I tree, giving us much better > incite into presence of our haplogroup in northern Europe 8000 years ago. > I have sent several sets of the confirmed phylogenetically equivalent snp > lists to them and hopefully they will see if they are readable for Motala2 > and Motala9. > > What I have not put together yet, waiting to see if they will use it or > that Motala2 and Motala9 are not confirmed to be part of I2....., is the > very huge list of firmly confirmed phyloequivalent snps to M253 and P40 > (I1 snps). Since that branch line segment is so long, 22000 years ago up > to 4500 years ago, the list of well confirmed equivalent snps is probably > presently approaching 100 in number. If Motala2 or Motala9 are confirmed > I2..... then no sense checking them on all those I1 snps. > > So there could be much more of value to be extracted from these ancient > dna samples from a complete use of their full genome measurements plus the > hobby community’s most up to date list of well confirmed and well placed > ysnps. > I hope they will continue to work with us as they did on the initial set > of ysnps equivalent to M423 and L178 which produced such informative > results. > > Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited > paper concluded, then a complete list of phylogenetically equivalent snps > to P38 should probably be tested to see if he is haplogroup I or not? > > > > > > > > > > Kenneth Nordtvedt > > Haplogroup I Clade Modalities and Trees at: > http://knordtvedt.home.bresnan.net > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Well, here is a little update on my own GENO2.0 results since I arrived home and was able to go back and find the raw data call and I see that in my November 2013 data the report was derived but showed PF3514 as A->G in both my I2 raw results and the I1 raw results for the others in my project. I see that that is just old news now and is exactly what Obed wrote. Sorry to have bothered you with unhelpful data. It did point to an upstream position which is now nicely confirmed by the data Magoon has provided for all of us. Thanks Richard On Wed, Jan 8, 2014 at 2:00 PM, DNAresults <[email protected]> wrote: > John, > > I might be missing something here, but I agree with Obed -- I am I2b1c > (I-P78) and I have PF 3514 derived (+) from GENO 2.0 as do all the I1d > (I-L22) members of my surname project who tested with GENO 2.0. I don't > have immediate access to the call right now to see if it shows a "C" but I > believe it does. So, no new SNP eh? > > Richard Brewer > > > On Wednesday, January 8, 2014, Obed W Odom wrote: > >> John, I wouldn't call PF3514=C a new SNP. I am I1-Z138 and also have C. In >> fact, the ISOGG Y browser says this SNP is at the IJ level in the Y tree >> so >> probably all I and J people should have it. The problem seems to be that >> the original reference for PF3514 showed A to G instead of A to C. All of >> the next-generation-sequencing results that I have seen for I1 and !2 >> people show C. >> >> >> On Wed, Jan 8, 2014 at 2:21 PM, John O'Grady <[email protected] >> >wrote: >> >> > Bernie, >> > The reason that the Geno 2.0 chip didn't work is that the PF3514 >> mutation >> > is A to C, not A to G. The good news is that, according to Full >> Genomes, I >> > am PF3514=C+. So we have a new SNP for L161-Isles. >> > John O'Grady >> > >> > >> >> ------------------------------- >> To unsubscribe from the list, please send an email to >> [email protected] with the word 'unsubscribe' >> without the quotes in the subject and the body of the message >> >

John, I wouldn't call PF3514=C a new SNP. I am I1-Z138 and also have C. In fact, the ISOGG Y browser says this SNP is at the IJ level in the Y tree so probably all I and J people should have it. The problem seems to be that the original reference for PF3514 showed A to G instead of A to C. All of the next-generation-sequencing results that I have seen for I1 and !2 people show C. On Wed, Jan 8, 2014 at 2:21 PM, John O'Grady <[email protected]>wrote: > Bernie, > The reason that the Geno 2.0 chip didn't work is that the PF3514 mutation > is A to C, not A to G. The good news is that, according to Full Genomes, I > am PF3514=C+. So we have a new SNP for L161-Isles. > John O'Grady > >

And I made a @#$%% typo. Motala2 is M253- of course. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net -----Original Message----- From: Kenneth Nordtvedt Sent: Wednesday, January 08, 2014 2:22 PM To: [email protected] Subject: [yDNAhgI] phyloequivalent ysnps In my recent message about ancient haplogroup I in Europe I forgot to include a comment on phyloequivalent snps. Here it is. So you can see the importance in Tree building of keeping track of the full list of phyloequivalent snps for every branch segment of the Tree, especially as the branch segments are further upstream. As the business of recovering the most complete ydna as possible for very old bones continues, and we want to extract information from those reconstructed y chromosomes, necessarily the reconstructions will be incomplete to various degrees depending on soils and climate conditions, etc. Not all snp sites will be readable. So as complete as possible a list of phyloequivalent snps in our Tree gives the most number of alternative sites to read in the reconstructed ydna of the ancients. This will allow for more information extracted from that ancient dna for better location of the ancient dna in the Tree. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

I think Geno 2.0 has recalibrated/fixed PF3514 recently. I have multiple PF3514=A,A in I-P37.2 since November, before that they were almost all A G. Bernie

In my recent message about ancient haplogroup I in Europe I forgot to include a comment on phyloequivalent snps. Here it is. So you can see the importance in Tree building of keeping track of the full list of phyloequivalent snps for every branch segment of the Tree, especially as the branch segments are further upstream. As the business of recovering the most complete ydna as possible for very old bones continues, and we want to extract information from those reconstructed y chromosomes, necessarily the reconstructions will be incomplete to various degrees depending on soils and climate conditions, etc. Not all snp sites will be readable. So as complete as possible a list of phyloequivalent snps in our Tree gives the most number of alternative sites to read in the reconstructed ydna of the ancients. This will allow for more information extracted from that ancient dna for better location of the ancient dna in the Tree. Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net

Richard, I am always looking for new SNPs. Sometimes I get a little overenthusiastic. I will be right one of these times. John O'Grady > > John, > > I might be missing something here, but I agree with Obed -- I am I2b1c > (I-P78) and I have PF 3514 derived (+) from GENO 2.0 as do all the I1d > (I-L22) members of my surname project who tested with GENO 2.0. I don't > have immediate access to the call right now to see if it shows a "C" but I > believe it does. So, no new SNP eh? > > Richard Brewer

Did you find out any more info on the current Russian sample that was supposed to be similar to one of the old samples? On Wednesday, January 8, 2014 1:20 PM, Kenneth Nordtvedt <[email protected]> wrote: Here’s an update on what has recently been learned about haplogroup I ydna in ancient Europe.  Bones of several males from 8000 b.p. were examined for their dna:  Loschbour was from a Luxuemberg site, four male dna Motala 2,3,9,12 were from a Swedish site.  Another male from Swedish site, Motala6, seems not to be confirmed haplogroup I, but his true haplogroup is still unidentified though thought Q for awhile.  Their ydna analysis of these ancient males is discussed in depth in the paper “Ancient human genomes suggest three ancestral populations for presentday Europeans”. As of a month ago, the hobby community had collected a number of phyloequivalent ysnps to M423, mainly from Geno2:  the full list is M423, L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, CTS1293, CTS11030. Multiple customers of Geno2 chip or WTY and  from the L161 “Isles” clades or from the L621 “Dinaric” clade were found derived for ALL of these 12 ysnps.  Everyone else in haplogroup I was found ancestral for All of them. In the cited paper, however, only L178 and M423 were tested on these ancient dna samples.  They took their snps to test from ISOGG list, and as we know that list always lags present knowledge because of the procedure of inclusion into their list.  The ancient dna samples are not necessarily readable on any given snp site, so it is important to have that ancient dna tested on alternative sites of equivalence if unreadable on any particular site.  So I sent the 10 snp sites listed above for which they did not test to authors of the cited paper.  They very kindly looked up the allele values for the additional snps which could be read. Loschbour was readable for all 12 snps with results:  derived for CTS8239, CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other five snps including L1224. Motala12 was readable for 9 of the 12 snps with results which exactly matched Loschbour.  Unreadable snps were CTS8239, L1224, M423. Motala3 was readable for only 3 of the 12 snps with results matching Loschbour: CTS7218+, CTS176+, CTS1293+ Motala2 was readable for only 1 of the 12 snps and disagreed with first three dna samples, being CTS1293- Motala9 was not readable for any of the 12 snps. Loschbour and Motala12 (and probably Motala3) establish a new branch line of the I Tree which is today probably extinct or severely tiny in present  population.  It splits the 12 snps into ancestrals and deriveds.  See “Tree and Map for haplogroup I” for position of this new  branch of the tree. So we concentrate on what we might further learn about Motala2 and Motala9 samples using the rich catalog of well placed ysnps that has resulted from Geno2 and other products done by hobbyists. All we know about Motala9 is that he is P38+ but P40-.  All we know about Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-.  So both are haplogroup I, but that’s about all we know. Motala9 could be most anything within haplogroup I except a modern I1.  He could be anything in I2...... and could be a new ancient branch on the ancestral I1 line which branched off prior to P40.  That’s a time range of 22,000 years b.p. up to about 4500 years b.p.  Similarly Motala2 could have branched off of the ancestral I1 line anytime before M253, and Motala still has much of I2...... for his location. So there is much work that authors of this paper can do using our Geno2 generated rich lists of phylogenetically equivalent snps for many of the key branch segments of the I tree.  Motala2 and Motala9 could conceivably be placed fairly well in the haplogroup I tree, giving us much better incite into presence of our haplogroup in northern Europe 8000 years ago.  I have sent several sets of the confirmed phylogenetically equivalent snp lists to them and hopefully they will see if they are readable for Motala2 and Motala9. What I have not put together yet, waiting to see if they will use it or that Motala2 and Motala9 are not confirmed to be part of I2....., is the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 snps).  Since that branch line segment is so long, 22000 years ago up to 4500 years ago, the list of well confirmed equivalent snps is probably presently approaching 100 in number.  If Motala2 or Motala9 are confirmed I2..... then no sense checking them on all those I1 snps. So there could be much more of value to be extracted from these ancient dna samples from a complete use of their full genome measurements plus the hobby community’s most up to date list of well confirmed and well placed ysnps. I hope they will continue to work with us as they did on the initial set of ysnps equivalent to M423 and L178 which produced such informative results. Footnote:  If Motala6 is indeed not confirmed haplogroup Q as the cited paper concluded, then a complete list of phylogenetically equivalent snps to P38 should probably be tested to see if he is haplogroup I or not? Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net/ ------------------------------- To unsubscribe from the list, please send an email to [email protected] with the word 'unsubscribe' without the quotes in the subject and the body of the message

Here’s an update on what has recently been learned about haplogroup I ydna in ancient Europe. Bones of several males from 8000 b.p. were examined for their dna: Loschbour was from a Luxuemberg site, four male dna Motala 2,3,9,12 were from a Swedish site. Another male from Swedish site, Motala6, seems not to be confirmed haplogroup I, but his true haplogroup is still unidentified though thought Q for awhile. Their ydna analysis of these ancient males is discussed in depth in the paper “Ancient human genomes suggest three ancestral populations for presentday Europeans”. As of a month ago, the hobby community had collected a number of phyloequivalent ysnps to M423, mainly from Geno2: the full list is M423, L178, L1224, CTS8486, CTS8239, CTS7218, CTS5985, CTS5375, CTS1802, CTS176, CTS1293, CTS11030. Multiple customers of Geno2 chip or WTY and from the L161 “Isles” clades or from the L621 “Dinaric” clade were found derived for ALL of these 12 ysnps. Everyone else in haplogroup I was found ancestral for All of them. In the cited paper, however, only L178 and M423 were tested on these ancient dna samples. They took their snps to test from ISOGG list, and as we know that list always lags present knowledge because of the procedure of inclusion into their list. The ancient dna samples are not necessarily readable on any given snp site, so it is important to have that ancient dna tested on alternative sites of equivalence if unreadable on any particular site. So I sent the 10 snp sites listed above for which they did not test to authors of the cited paper. They very kindly looked up the allele values for the additional snps which could be read. Loschbour was readable for all 12 snps with results: derived for CTS8239, CTS7218, CTS5985, CTS176, CTS1293, L178, M423, but ancestral for the other five snps including L1224. Motala12 was readable for 9 of the 12 snps with results which exactly matched Loschbour. Unreadable snps were CTS8239, L1224, M423. Motala3 was readable for only 3 of the 12 snps with results matching Loschbour: CTS7218+, CTS176+, CTS1293+ Motala2 was readable for only 1 of the 12 snps and disagreed with first three dna samples, being CTS1293- Motala9 was not readable for any of the 12 snps. Loschbour and Motala12 (and probably Motala3) establish a new branch line of the I Tree which is today probably extinct or severely tiny in present population. It splits the 12 snps into ancestrals and deriveds. See “Tree and Map for haplogroup I” for position of this new branch of the tree. So we concentrate on what we might further learn about Motala2 and Motala9 samples using the rich catalog of well placed ysnps that has resulted from Geno2 and other products done by hobbyists. All we know about Motala9 is that he is P38+ but P40-. All we know about Motala2 is that he is P38+ M253+ Z79- L703- L37- L621-. So both are haplogroup I, but that’s about all we know. Motala9 could be most anything within haplogroup I except a modern I1. He could be anything in I2...... and could be a new ancient branch on the ancestral I1 line which branched off prior to P40. That’s a time range of 22,000 years b.p. up to about 4500 years b.p. Similarly Motala2 could have branched off of the ancestral I1 line anytime before M253, and Motala still has much of I2...... for his location. So there is much work that authors of this paper can do using our Geno2 generated rich lists of phylogenetically equivalent snps for many of the key branch segments of the I tree. Motala2 and Motala9 could conceivably be placed fairly well in the haplogroup I tree, giving us much better incite into presence of our haplogroup in northern Europe 8000 years ago. I have sent several sets of the confirmed phylogenetically equivalent snp lists to them and hopefully they will see if they are readable for Motala2 and Motala9. What I have not put together yet, waiting to see if they will use it or that Motala2 and Motala9 are not confirmed to be part of I2....., is the very huge list of firmly confirmed phyloequivalent snps to M253 and P40 (I1 snps). Since that branch line segment is so long, 22000 years ago up to 4500 years ago, the list of well confirmed equivalent snps is probably presently approaching 100 in number. If Motala2 or Motala9 are confirmed I2..... then no sense checking them on all those I1 snps. So there could be much more of value to be extracted from these ancient dna samples from a complete use of their full genome measurements plus the hobby community’s most up to date list of well confirmed and well placed ysnps. I hope they will continue to work with us as they did on the initial set of ysnps equivalent to M423 and L178 which produced such informative results. Footnote: If Motala6 is indeed not confirmed haplogroup Q as the cited paper concluded, then a complete list of phylogenetically equivalent snps to P38 should probably be tested to see if he is haplogroup I or not? Kenneth Nordtvedt Haplogroup I Clade Modalities and Trees at: http://knordtvedt.home.bresnan.net